SGCG

sarcoglycan gamma

Basic information

Region (hg38): 13:23180978-23325162

Previous symbols: [ "DMDA1", "MAM", "LGMD2C" ]

Links

ENSG00000102683 ∙ NCBI:6445 ∙ OMIM:608896 ∙ HGNC:10809 ∙ Uniprot:Q13326 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive limb-girdle muscular dystrophy type 2C (Definitive), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type 2C (Strong), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type 2C (Supportive), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type 2C (Definitive), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy, limb-girdle, limb-girdle, autosomal recessive, 5	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal	1303286; 7481775; 8923014; 8968757; 10507732; 10720277; 16832103; 18285821

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SGCG gene.

• Autosomal recessive limb-girdle muscular dystrophy type 2C (368 variants)
• not provided (154 variants)
• Sarcoglycanopathy (38 variants)
• not specified (36 variants)
• Limb-Girdle Muscular Dystrophy, Recessive (20 variants)
• Charlevoix-Saguenay spastic ataxia (6 variants)
• Autosomal recessive limb-girdle muscular dystrophy (4 variants)
• Inborn genetic diseases (3 variants)
• - (2 variants)
• Abnormality of the musculature (1 variants)
• Primary dilated cardiomyopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGCG gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	71	2	77
missense	2	3	124	2	1	132
nonsense	10	9	1			20
start loss						0
frameshift	21	18				39
inframe indel			2			2
splice donor/acceptor (+/-2bp)	3	16	2			21
splice region	1		10	16	2	29
non coding			8	65	36	109
Total	36	46	141	138	39

Highest pathogenic variant AF is 0.000158

Variants in SGCG

This is a list of pathogenic ClinVar variants found in the SGCG region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
13-23180988-G-A		Limb-Girdle Muscular Dystrophy, Recessive • Sarcoglycanopathy	Benign/Likely benign (Nov 19, 2019)
13-23181070-T-C		Sarcoglycanopathy • Limb-Girdle Muscular Dystrophy, Recessive • not specified • SGCG-related disorder	Conflicting classifications of pathogenicity (Mar 01, 2024)
13-23181080-G-A		Autosomal recessive limb-girdle muscular dystrophy type 2C	Uncertain significance (Apr 13, 2022)
13-23181294-T-C			Likely benign (May 24, 2021)
13-23203416-A-T			Likely benign (Sep 04, 2018)
13-23203451-T-G			Likely benign (Sep 05, 2018)
13-23203521-A-C			Likely benign (Sep 05, 2018)
13-23203603-C-T			Likely benign (Sep 05, 2018)
13-23203687-C-T		not specified	Conflicting classifications of pathogenicity (Feb 04, 2016)
13-23203692-C-T		Autosomal recessive limb-girdle muscular dystrophy type 2C	Uncertain significance (Nov 10, 2021)
13-23203699-T-C		Autosomal recessive limb-girdle muscular dystrophy type 2C	Uncertain significance (Aug 03, 2022)
13-23203701-C-T		Autosomal recessive limb-girdle muscular dystrophy type 2C	Uncertain significance (Jul 15, 2022)
13-23203702-G-A		Autosomal recessive limb-girdle muscular dystrophy type 2C	Uncertain significance (Oct 13, 2022)
13-23203704-G-T		Autosomal recessive limb-girdle muscular dystrophy type 2C	Likely pathogenic (Oct 24, 2023)
13-23203711-A-G		Autosomal recessive limb-girdle muscular dystrophy type 2C • Sarcoglycanopathy	Uncertain significance (Mar 05, 2023)
13-23203716-A-G		Autosomal recessive limb-girdle muscular dystrophy type 2C • Inborn genetic diseases	Uncertain significance (Sep 01, 2022)
13-23203721-C-T		Autosomal recessive limb-girdle muscular dystrophy type 2C	Likely benign (Feb 01, 2022)
13-23203728-G-A		Autosomal recessive limb-girdle muscular dystrophy type 2C	Uncertain significance (Apr 02, 2019)
13-23203732-T-A		Inborn genetic diseases	Uncertain significance (Aug 28, 2023)
13-23203736-C-T		Autosomal recessive limb-girdle muscular dystrophy type 2C	Likely benign (Jan 27, 2024)
13-23203738-T-C		Autosomal recessive limb-girdle muscular dystrophy type 2C	Uncertain significance (Jun 02, 2021)
13-23203739-A-G		Autosomal recessive limb-girdle muscular dystrophy type 2C	Uncertain significance (Aug 05, 2021)
13-23203740-G-C		Autosomal recessive limb-girdle muscular dystrophy type 2C	Uncertain significance (Mar 08, 2022)
13-23203751-G-A		Autosomal recessive limb-girdle muscular dystrophy type 2C	Likely benign (Sep 19, 2023)
13-23203751-G-T		Autosomal recessive limb-girdle muscular dystrophy type 2C	Uncertain significance (Aug 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGCG	protein_coding	protein_coding	ENST00000218867	7	144214

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000482	0.876	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.134	168	163	1.03	0.00000874	1881
Missense in Polyphen		64	65.214	0.98139		773
Synonymous	-1.14	73	61.6	1.18	0.00000359	562
Loss of Function	1.44	9	15.0	0.600	7.03e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000667	0.000666
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000193	0.000193
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000989	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the sarcoglycan complex, a subcomplex of the dystrophin-glycoprotein complex which forms a link between the F-actin cytoskeleton and the extracellular matrix.
• Pathway: Dilated cardiomyopathy (DCM) - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Arrhythmogenic Right Ventricular Cardiomyopathy (Consensus)

Recessive Scores

• pRec: 0.363

Intolerance Scores

• loftool: 0.314
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.390
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0893

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sgcg
• Phenotype: growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype

Gene ontology

• Biological process: muscle organ development;cardiac muscle tissue development;heart contraction
• Cellular component: nucleoplasm;cytoplasm;cytoskeleton;plasma membrane;sarcoglycan complex;integral component of membrane;sarcolemma
• Molecular function: protein binding